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Tropical forests are incredibly diverse in structure and function. Despite, or perhaps because of, this diversity, tropical biologists often conduct research exclusively in one or perhaps a few forest types. Rarely do we study the ecotone—the interstitial region between forest types. Ecotones are hyper-diverse, dynamic systems that control the flow of energy and organisms between adjacent ecosystems, with their locations determined by species' physiological limits. In this review, we describe how studying ecotones can provide key indicators for monitoring the state of Neotropical forests from organisms to ecosystems. We first describe how ecotones have been studied in the past and summarize our current understanding of tropical ecotones. Next, we provide three example lines of research focusing on the ecological and evolutionary dynamics of the ecotone between tropical dry forests and desert; between tropical dry and rainforests; and between Cerrado and Atlantic rainforests, with the latter being a particularly well-studied ecotone. Lastly, we outline methods and tools for studying ecotones that combine remote sensing, new statistical techniques, and field-based forest dynamics plot data, among others, for understanding these important systems. [ABSTRACT FROM AUTHOR]

New World monkeys (NWM) comprise a group of extant and extinct taxa exclusive to the Neotropics. Lineage dispersal modeling was employed to test the validity of previously reported biogeographic patterns in NWM. Specifically, this research sought to confirm whether the dispersal timings of these patterns were supported by the modeling results. Species geographic distributions of extant platyrrhines were used to obtain a bioregionalization scheme. A lineage dispersal model was constructed based on multiple-area range, likelihood inference of rate, and stochastic mapping under likelihood. Based on published phylogenies, ten trees were randomly sampled and, for each tree, ten stochastic mappings were simulated. Results were presented as event counts and averages across the 100 stochastic mappings, and the timings of the inferred dispersal routes were compared to the timings of 12 biogeographic pattern hypotheses gathered from the literature. The modeling analysis provided directional and temporal support for eleven of the twelve patterns. Lineages most frequently dispersed from Western Amazonia towards other bioregions. For four dispersal routes, events initiated earlier than previously reported. The Western Amazonia bioregion served as both the ancestral area and primary source of platyrrhine lineages. Analyses revealed a novel biogeographic pattern, namely the “Amazonian eastward” dispersal route, which started in the Miocene epoch, during the establishment of the transcontinental Amazon River system, and lasted until recently in an increasing trend of dispersal rate. This route showed the greatest number of dispersal events during the macroevolution of NWM. [ABSTRACT FROM AUTHOR]

Tropical forests are incredibly diverse in structure and function. Despite, or perhaps because of, this diversity, tropical biologists often conduct research exclusively in one or perhaps a few forest types. Rarely do we study the ecotone—the interstitial region between forest types. Ecotones are hyper-diverse, dynamic systems that control the flow of energy and organisms between adjacent ecosystems, with their locations determined by species’ physiological limits. In this review, we describe how studying ecotones can provide key indicators for monitoring the state of Neotropical forests from organisms to ecosystems. We first describe how ecotones have been studied in the past and summarize our current understanding of tropical ecotones. Next, we provide three example lines of research focusing on the ecological and evolutionary dynamics of the ecotone between tropical dry forests and desert; between tropical dry and rainforests; and between Cerrado and Atlantic rainforests, with the latter being a particularly well-studied ecotone. Lastly, we outline methods and tools for studying ecotones that combine remote sensing, new statistical techniques, and field-based forest dynamics plot data, among others, for understanding these important systems.

Observations of the annual cycle of atmospheric CO2 in high northern latitudes provide evidence for an increase in terrestrial metabolism in Arctic tundra and boreal forest ecosystems. However, the mechanisms driving these changes are not yet fully understood. One proposed hypothesis is that ecological change from disturbance, such as wildfire, could increase the magnitude and change the phase of net ecosystem exchange through shifts in plant community composition. Yet, little quantitative work has evaluated this potential mechanism at a regional scale. Here we investigate how fire disturbance influences landscape‐level patterns of photosynthesis across western boreal North America. We use Alaska and Canadian large fire databases to identify the perimeters of wildfires, a Landsat‐derived land cover time series to characterize plant functional types (PFTs), and solar‐induced fluorescence (SIF) from the Orbiting Carbon Observatory‐2 (OCO‐2) as a proxy for photosynthesis. We analyze these datasets to characterize post‐fire changes in plant succession and photosynthetic activity using a space‐for‐time approach. We find that increases in herbaceous and sparse vegetation, shrub, and deciduous broadleaf forest PFTs during mid‐succession yield enhancements in SIF by 8–40% during June and July for 2‐ to 59‐year stands relative to pre‐fire controls. From the analysis of post‐fire land cover changes within individual ecoregions and modeling, we identify two mechanisms by which fires contribute to long‐term trends in SIF. First, increases in annual burning are shifting the stand age distribution, leading to increases in the abundance of shrubs and deciduous broadleaf forests that have considerably higher SIF during early‐ and mid‐summer. Second, fire appears to facilitate a long‐term shift from evergreen conifer to broadleaf deciduous forest in the Boreal Plain ecoregion. These findings suggest that increasing fire can contribute substantially to positive trends in seasonal CO2 exchange without a close coupling to long‐term increases in carbon storage. [ABSTRACT FROM AUTHOR]

Given accelerated dryland expansion, studies on aridity‐driven desertification are of great importance for advancing our understanding of land degradation mechanisms and developing possible mitigation measures. However, the mechanism by which increased aridity drives ecosystems toward desertification and the impacts of aridity on desertification vulnerability both in space and over time remain unclear. Here, we collected eight key ecosystem structure/functioning data (including soil, vegetation, and animal) for threshold identification using piecewise linear models, and then linked them to biome shifts to explore the process of aridity‐driven desertification. The results show that ecosystems along aridity index (AI, 1 − precipitation/potential evapotranspiration) gradients experience three vulnerable stages featuring different threshold and biome responses: a low vulnerability stage (AI: 0.5–0.65; mainly featuring a soil fertility loss and a forest decline), a moderate vulnerability stage (AI: 0.65–0.75; mainly featuring accelerated non‐forest vegetation degradation) and a high vulnerability stage (AI: 0.75–1; mainly featuring rapid overall land degradation). According to further simulations, areas with low to high vulnerability account for 31% of the global terrestrial area, which is projected to increase by 18.8% (21.2%) by the end of the 21st century under the greenhouse gas emission scenario SSP2‐4.5 (SSP3‐7.0). Given increased vulnerability and population growth, Africa and East Asia are exposed to great desertification risk and ensuing contradiction between humans and land. These findings can provide a theoretical and practical reference for ecosystem management and policy development, which are critical for dryland ecological security and human welfare in areas threatened by desertification. [ABSTRACT FROM AUTHOR]

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The persistent spread of shrublands is a global phenomenon observed across semiarid grassland-shrubland boundaries. Observations in South Africa, however, have detected a contrasting trend of increasing grass cover across the transition between the Nama-Karoo and Grassland Biomes over the last few decades. A west-to-east gradient of increasing mean annual rainfall, and underlying geology, controls the natural transition of Karoo dwarf shrublands to semiarid grasslands. The availability of historical vegetation surveys and landscape photographs, weather, and livestock census records, made it possible to assess the nature, extent, and drivers of vegetation change across this biome transition. Rainfall has been generally higher over the last four decades compared to the years prior to the original surveys. This, together with a reduction in livestock numbers, is the main driver of the westward expansion by ∼100 km of perennial grasses, and a general increase in dwarf shrub and total vegetation cover. Rangeland condition, as indexed by estimates of grazing capacity, has improved significantly. Despite a structural shift towards grassland-dominance, the original species complement has persisted. The rainfall-driven increase in grass fuel loads in the region, however, places these rangelands at risk of becoming altered by increasing fire frequency. [ABSTRACT FROM AUTHOR]

Tropical America (the Neotropics) is the most biodiverse realm on Earth and might harbour more species than tropical Asia and Africa combined. The evolutionary history generating this outstanding diversity remains poorly understood partly because data on the geographic distribution of species is scarce. Collections from museums and herbaria can overcome this gap, but uncertain data quality hampers their use, especially in historical biogeography. Here, I highlight the results from recent studies quantifying diversification and bioregion connectivity in the Neotropics using large-scale species occurrence data, and argue that (i) recently developed software to analyse large-scale data provides a methodological route forward for biogeography, and (ii) biotic connectivity within and among bioregions is a common, but underappreciated, process in the evolution of Neotropical diversity.

Where each species actually lives is distinct from where it could potentially survive and persist. This suggests that it may be important to distinguish established from enabled biome affinities when considering how ancestral species moved and evolved among major habitat types. We introduce a new phylogenetic method, called RFBS, to model how anagenetic and cladogenetic events cause established and enabled biome affinities (or, more generally, other discrete realized versus fundamental niche states) to shift over evolutionary timescale. We provide practical guidelines for how to assign established and enabled biome affinity states to extant taxa, using the flowering plant clade Viburnum as a case study. Through a battery of simulation experiments, we show that RFBS performs well, even when we have realistically imperfect knowledge of enabled biome affinities for most analyzed species. We also show that RFBS reliably discerns established from enabled affinities, with similar accuracy to standard competing models that ignore the existence of enabled biome affinities. Lastly, we apply RFBS to Viburnum to infer ancestral biomes throughout the tree and to highlight instances where repeated shifts between established affinities for warm and cold temperate forest biomes were enabled by a stable and slowly-evolving enabled affinity for both temperate biomes.

Rhytiphora Audinet-Serville, 1835 is the most speciose longhorn beetle (Cerambycidae Latreille, 1802) genus in Australia, with ~200 species (from nearly 40 former genera, now synonymised into one) distributed across the entire continent. We used mitochondrial genome data from whole genome shotgun sequencing and COI barcoding of museum specimens to reconstruct the phylogeny of 68 Rhytiphora species, and analysed the morphological diversity and biogeographic history. We recovered a monophyletic Rhytiphora containing two distinct clades, within which all of the former genera (except Achriotypa Pascoe, 1875) are paraphyletic. Nine morphological traits (including body size and the male setose 'sex patches') show strong phylogenetic signal and can be used to differentiate between the two clades. One clade is mainly restricted to Australia's tropical north, whereas the other, larger clade has many species along the mesic east coast. Both clades have experienced multiple biome shifts, displaying a remarkable flexibility in habitat occupancy. [ABSTRACT FROM AUTHOR]

Various facets of global changes and related problems and challenges are asking for sound impact assessments and corresponding coping strategies. The human impact on nature is a major driver of biodiversity loss and restricted ecosystem functioning and services. Assessing such global changes is often done by using biomes as benchmarks. However, even if the wording and terminology seem common sense ('tropical rain forest', 'steppe', 'boreal forest') global biome units and maps deviate in many ways. This is well justified by their individual intention, expert opinions, disciplinary background, and methodology of creation. A closer look reveals linkages between spatial accordance and common origin in climate classifications and maps. Their original influence, however, is rarely evident. In consequence, it is difficult if not impossible for users to realize and understand differences in these global maps. Furthermore, it is difficult to accept the fact that there is no common standard for global biomes. Even more surprising is the fact that some approaches are uncritically taken for common sense and are perpetuated over decades. This study aims to review established global biome concepts. Regions that are consistently assigned to comparable types of biomes shall be detected and also regions where ambiguity exists. For this purpose, we shortly review the history of existing concepts and the generic relations between them. Biomes, ecozones and climate classifications are considered. We digitized the most prominent biome classifications. Spatial match and mismatch between concepts were analyzed globally. We detect areas of spatial agreement and regions with ambiguous classifications. A clustering approach including 287 individual biomes originating from 12 established global biome concepts and their classifications/units revealed 12 terrestrial biome clusters among which 8 can be assigned to terrestrial ecological units. One cluster on ice caps adds to this. And finally, 3 clusters represent rather transition zones (ecotones), high mountain plateaus or are of minor areal extent. The spatial arrangement of these emerging clusters is displayed on a global map. Additionally, regions of uncertainty related to class assignment were identified. Those primarily occur in the vicinity of mountainous regions. The findings of this study should be seen as a work in progress and as a basis for further optimization of global biome concepts. [ABSTRACT FROM AUTHOR]

The dating of diversification events, including transitions between biomes, is key to elucidate the processes that underlie the assembly and evolution of tropical biodiversity. Afzelia is a widespread genus of tropical trees, threatened by exploitation for its valuable timber, that presents an interesting system to investigate diversification events in Africa. Africa hosts diploid Afzelia species in the savannahs north and south of the Guineo-Congolian rainforest and autotetraploid species confined to the rainforest. Species delimitation and phylogenetic relationships among the diploid and tetraploid species remained unresolved in previous studies using small amounts of DNA sequence data. We used genotyping-by-sequencing in the five widespread Afzelia species in Africa, the savannah species A. africana and A. quanzensis and the rainforest species A. bipindensis, A. pachyloba, and A. bella. Maximum likelihood and coalescent approaches resolved all species as monophyletic and placed the savannah and rainforest taxa into two separate clades corresponding to contrasted ploidy levels. Our data are thus compatible with a single biome shift in Afzelia in Africa, although we were unable to conclude on its direction. SNAPP calibrated species trees show that the savannah diploids started to diversify early, at 12 (9.09–14.89) Ma, which contrasts with a recent and rapid diversification of the rainforest tetraploid clade, starting at 4.22 (3.12 – 5.36) Ma. This finding of older diversification in a tropical savannah clade vs. its sister rainforest clade is exceptional; it stands in opposition to the predominant observation of young ages for savannahs lineages in tropical regions during the relatively recent expansion of the savannah biome.

Terrestrial ecosystems respond to climate change in various ways, making it crucial to improve our understanding of these dynamics and uncertainty in projections. Here, we investigate how the species composition in a temperate-subtropical mixed forest on Jeju Island, South Korea, would change by 2099 and analysed the resultant effects on phenological timings and carbon flux using an individual cohort-based model—the ecosystem demography biosphere model version 2. We use the analyses of variance to decompose the contribution of model parameters (four sets) and climate inputs (four global climate models under four representative concentration pathway (RCP) scenarios) to the total uncertainty in the leaf area index (LAI) and net ecosystem productivity (NEP) projections. We find that with increases in temperature, photosynthetically active radiation, and vapour pressure deficit, the dominance of subtropical species will gradually increase by approximately 11%, from 30.2% in 2013 to 41.1% by the end of this century, yet there was a large variation in the projections depending on the model parameter and climate inputs. We also show the increases in the LAI and length of growing season by the end of this century, resulting in an increased NEP at the rate of up to 62.7 gC m ^−2 yr ^−1 per decade under the RCP8.5. The uncertainty in the LAI projection was largely due to the model parameter (and its interaction with climate inputs); however, the uncertainty contribution of climate models is as large as the emission scenario in the NEP projection. This study highlights the importance of identifying uncertainty sources for a robust projection of terrestrial ecosystem and carbon cycle.

The dating of diversification events, including transitions between biomes, is key to elucidate the processes that underlie the assembly and evolution of tropical biodiversity. Afzelia is a widespread genus of tropical trees, threatened by exploitation for its valuable timber, that presents an interesting system to investigate diversification events in Africa. Africa hosts diploid Afzelia species in the savannahs north and south of the Guineo-Congolian rainforest and autotetraploid species confined to the rainforest. Species delimitation and phylogenetic relationships among the diploid and tetraploid species remained unresolved in previous studies using small amounts of DNA sequence data. We used genotyping-by-sequencing in the five widespread Afzelia species in Africa, the savannah species A. africana and A. quanzensis and the rainforest species A. bipindensis , A. pachyloba , and A. bella. Maximum likelihood and coalescent approaches resolved all species as monophyletic and placed the savannah and rainforest taxa into two separate clades corresponding to contrasted ploidy levels. Our data are thus compatible with a single biome shift in Afzelia in Africa, although we were unable to conclude on its direction. SNAPP calibrated species trees show that the savannah diploids started to diversify early, at 12 (9.09–14.89) Ma, which contrasts with a recent and rapid diversification of the rainforest tetraploid clade, starting at 4.22 (3.12 – 5.36) Ma. This finding of older diversification in a tropical savannah clade vs. its sister rainforest clade is exceptional; it stands in opposition to the predominant observation of young ages for savannahs lineages in tropical regions during the relatively recent expansion of the savannah biome. [ABSTRACT FROM AUTHOR]

Aim: To quantify evolutionary transitions between tropical evergreen rain forest and seasonally dry biomes, to test whether biome transitions affect lineage diversification and to examine the robustness of these results to methodological choices. Location: The tropics. Time period: The Cenozoic. Major taxa studied: The plant subfamily Bombacoideae (Malvaceae). Methods: We inferred ancestral biomes based on a fossil‐dated molecular phylogeny of 103 species (59% of the clade) and recorded the number of transitions among biomes using biogeographical stochastic mapping based on the dispersal‐extinction‐cladogenesis model. We then estimated diversification rates using state‐specific speciation and extinction rate (SSE) methods. Furthermore, we tested the sensitivity of the results to model choice, phylogenetic uncertainty, measurement error and biome definition. Results: We found numerous transitions from evergreen rain forest to seasonally dry biomes, and fewer in the opposite direction. These results were robust to methodological choices. Biome type did not influence diversification rates, although this result was subject to uncertainty, especially related to model choice and biome definition. Main conclusions: Our results contradict the idea of evolutionary biome conservatism in Bombacoideae, and support previous findings that evergreen rain forests serve as a source for the flora of seasonally dry biomes. The impact of biome classification and biome definition on the results suggest caution when using a biome concept for biogeographical reconstruction and diversification rate analysis. [ABSTRACT FROM AUTHOR]

The monophyly of Boronia (Rutaceae) was tested using 134 accessions of 120 species belonging to 39 genera from subfamily Amyridoideae. Taxa included representatives of all eight sections of Boronia plus species of most genera in the two main clades related to Boronia that had been identified by earlier studies. These samples included a good representation of genera from both rainforest and sclerophyllous biomes. Maximum parsimony and Bayesian inference analyses were performed using three plastid markers (psbA‐trnH, trnL‐trnF, rbcL) and two nuclear ribosomal markers (ITS, ETS). Separate analyses of plastid and nuclear sequences using either maximum parsimony or Bayesian inference analyses recovered similar topologies. Apart from Boronia, the broad generic relationships of previous analyses were largely supported. Boronia is polyphyletic with section Cyanothamnus being more closely related to a large clade containing genera found in rainforest, including Melicope, Acronychia and their relatives. The remaining seven sections of Boronia formed a strongly supported and isolated group. Boronia sensu stricto is sister to a clade containing the Cyanothamnus‐Melicope‐Acronychia clade plus a clade containing Euodia, Zieria and other small genera found in rainforest or sclerophyllous communities. Issues with circumscriptions of ingroups and outgroups for previous analyses of Boronia and the complex relationship between Australasian genera found in rainforest and sclerophyllous communities are both discussed. Cyanothamnus is reinstated at generic level. Appropriate nomenclatural changes are made to transfer all currently recognised series, species, subspecies and varieties of Boronia sect. Cyanothamnus to the genus Cyanothamnus. [ABSTRACT FROM AUTHOR]

Summary: The extent to which phylogenetic biome conservatism vs biome shifting determines global patterns of biodiversity remains poorly understood. To address this question, we investigated the biogeography and trajectories of biome and growth form evolution across the Caesalpinia Group (Leguminosae), a clade of 225 species of trees, shrubs and lianas distributed across the Rainforest, Succulent, Temperate and Savanna Biomes. We focused especially on the little‐known Succulent Biome, an assemblage of succulent‐rich, grass‐poor, seasonally dry tropical vegetation distributed disjunctly across the Neotropics, Africa, Arabia and Madagascar.We reconstructed a time‐calibrated phylogeny, assembled species occurrence data and assigned species to areas, biomes and growth forms. These data are used to estimate the frequency of transcontinental disjunctions, biome shifts and evolutionary transitions between growth forms and test for phylogenetic biome conservatism and correlated evolution of growth forms and biome shifts.We uncovered a pattern of strong phylogenetic Succulent Biome conservatism. We showed that transcontinental disjunctions confined within the Succulent Biome are frequent and that biome shifts to the Savanna, Rainforest and Temperate Biomes are infrequent and closely associated with shifts in plant growth forms.Our results suggest that the Succulent Biome comprises an ecologically constrained evolutionary arena spanning large geographical disjunctions across the tropics. See also the Commentary on this article by Donoghue, 222: 1667–1669. [ABSTRACT FROM AUTHOR]

Highlights • Plastome and ribosomal DNA reveal two diversification periods (Miocene and Pleistocene) of African trees from genus Entandrophragma and Khaya. • Three biome transitions occurred from humid forest to dry or montane African forests. • Morphologically-based species delimitation is confirmed for Entandrophragma. Abstract Resolving phylogenetic relationships allows the investigation of how species diversity has evolved in various ecosystems. The genera Entandrophragma and Khaya consist of tree species distributed in different African biomes (lowland rain forest, dry forest and savanna, montane forest), and are suitable to examine how (single or multiple events) and when the processes of diversification led to biome transitions. Based on the sequencing of plastome (pDNA: c. 160,000 bp), ribosomal DNA (rDNA: c. 5300 bp), and habitat characteristic data for each species, we have: (i) reconstructed phylogenetic relationships between species and estimated the divergence period between the main lineages, and (ii) reconstructed ancestral states regarding biome preferences. The phylogenetic trees obtained with both markers support monophyly of the five sections of Entandrophragma previously defined based on fruit and floral characters. Nevertheless, the position of some species from the pDNA and rDNA tree topologies varied within sections. In Khaya, pDNA and rDNA show very divergent topologies, possibly due to a more recent diversification involving incomplete lineage sorting and/or recurrent hybridization events. Khaya diversified during the Pliocene and Pleistocene according to both markers; whereas, according to rDNA data, the Entandrophragma sections diverged during the early Miocene and species within sections diverged from the late Miocene to the Pleistocene. Divergence date estimates tended to be more recent using pDNA data. Biome transitions could not be reconstructed in Khaya as the species tree remains unresolved. Contrarily, three independent biome transitions were inferred in Entandrophragma. The first transition from rain to dry forests occurred during the Miocene and two other transitions were inferred during the Pleistocene, one from rain forest to dry forest and another from rain forest to mountain forest. Overall, we demonstrate that multiple biome transitions occurred, starting from a rain forest biome, possibly reflecting the global trend of aridification of Africa throughout the Cenozoic. [ABSTRACT FROM AUTHOR]

Summary: Cupressaceae subfamily Callitroideae has been an important exemplar for vicariance biogeography, but its history is more than just disjunctions resulting from continental drift. We combine fossil and molecular data to better assess its extinction and, sometimes, rediversification after past global change.Key fossils were reassessed and their phylogenetic placement for calibration was determined using trait mapping and Bayes Factors. Five vicariance hypotheses were tested by comparing molecular divergence times with the timing of tectonic rifting. The role of adaptation to fire (serotiny) in its spread across a drying Australia was tested for Callitris.Our findings suggest that three transoceanic disjunctions within the Callitroideae probably arose from long‐distance dispersal. A signature of extinction, centred on the end‐Eocene global climatic chilling and drying, is evident in lineages‐through‐time plots and in the fossil record. Callitris, the most diverse extant callitroid genus, suffered extinctions but surviving lineages adapted and re‐radiated into dry, fire‐prone biomes that expanded in the Neogene. Serotiny, a key adaptation to fire, likely evolved in Callitris coincident with the biome shift.Both extinction and adaptive shifts have probably played major roles in this chronicle of turnover and renewal, but better understanding of biogeographical history requires improved taxonomy of fossils. [ABSTRACT FROM AUTHOR]

Rainfall and grazing are primary drivers of vegetation composition in the Nama-Karoo. Increased rainfall increases grassiness, to where Nama-Karoo transitions to grassland. Severe grazing treatments (e.g. continuous or summer-only) increase abundance of grazing-tolerant dwarf shrubs and annual grasses, and decrease perennial grasses. Grootfontein, which is ecotonal between the Nama-Karoo and Grassland Biomes, houses long-term grazing trials. The area has experienced higher-than-average rainfall in recent decades. Plant basal cover data from the 1960s and 2010s allow several hypotheses to be addressed: (1) historical severe grazing (until 1985) will limit subsequent grassiness (grazing legacy effect); (2) severe grazing will preclude increases in grassiness, independent of rainfall (herbivore trap effect); and (3) historically leniently-grazed sites will transition to grassland with increased rainfall (biome shift effect). Rainfall was lower from 1957-1966 (350 mm) than from 2003-2012 (490 mm). The grazing legacy effect was supported based on the abundance of Aristida diffusa, despite all sites becoming much grassier. The herbivore trap effect was not supported. The biome shift effect was supported in that shifts to grassland sometimes occurred. Results suggest that increasing rainfall has prompted a shift to much increased grassiness and decreased abundance of dwarf shrubs, and that grazing had a smaller secondary effect. [ABSTRACT FROM AUTHOR]

The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understanding of how Neotropical biodiversity was assembled over evolutionary timescales. Here we infer the timing and origin of the living biota in all major Neotropical regions by performing a crosstaxonomic biogeographic analysis based on 4,450 species from six major clades across the tree of life (angiosperms, birds, ferns, frogs, mammals, and squamates), and integrate >1.3 million species occurrences with large-scale phylogenies. We report an unprecedented level of biotic interchange among all Neotropical regions, totaling 4,525 dispersal events. About half of these events involved transitions between major environmental types, with a predominant directionality from forested to open biomes. For all taxonomic groups surveyed here, Amazonia is the primary source of Neotropical diversity, providing >2,800 lineages to other regions. Most of these dispersal events were to Mesoamerica (~1,500 lineages), followed by dispersals into open regions of northern South America and the Cerrado and Chaco biomes. Biotic interchange has taken place for >60 million years and generally increased toward the present. The total amount of time lineages spend in a region appears to be the strongest predictor of migration events. These results demonstrate the complex origin of tropical ecosystems and the key role of biotic interchange for the assembly of regional biotas. [ABSTRACT FROM AUTHOR]

South Africa's biomes are characterized by their exceptional biodiversity and they provide important ecosystem services such as food, livestock production, medical plants or fuel wood to people. However, during recent decades, vegetation in South Africa experienced substantial changes and loss of biodiversity due to habitat loss, intensification of land use and climate change. The development of sustainable management policies requires an understanding of interactions between vegetation, climate change as well as land use and an identification of the areas most vulnerable to vegetation change. Here, we use the aDGVM, a dynamic vegetation model for tropical ecosystems, to investigate the risk of biome shifts in South Africa's Limpopo province under a set of IPCC climate change trajectories. The Limpopo province exemplifies an area highly susceptible to climate and land use change, where people in rural areas heavily rely on natural resources. We found a general trend towards more tree-dominated ecosystems and a particularly high risk of vegetation shift in more open grassland and savanna areas. The rate of biome shift is strongly linked to the IPCC scenario applied with the highest risk of biome shifts in the RCP 8.5 scenario. We conclude that, irrespective of future climate trajectories, management and conservation initiatives should particularly focus on these more open grassland and savanna ecosystems. [ABSTRACT FROM AUTHOR]

In the Anthropocene, alien species are no longer the only category of biological organism establishing and rapidly spreading beyond historical boundaries. We review evidence showing that invasions by native species are a global phenomenon and present case studies from Southern Africa, and elsewhere, that reveal how climate-mediated expansions of native plants into adjacent communities can emulate the functional and structural changes associated with invasions by alien plant species. We conclude that integrating native invasions into ecological practice and theory will improve mechanistic models and better inform policy and adaptive ecological management in the 21st century. [ABSTRACT FROM AUTHOR]

This article is a Commentary on Gagnon et al., 222: 1994–2008. [ABSTRACT FROM AUTHOR]

The Nama-Karoo is a semi-arid inland biome in South Africa dominated by dwarf shrubs with grasses, shrubs, geophytes and herbs at varying levels of abundance. The position of the Nama-Karoo/grassland boundary is determined in part by rainfall amount, and in recent years there has been an increase in grassiness, correlated with good rains. This has allowed wildfires, an unusual occurrence, to burn at several sites in the central and eastern regions of the biome. The general effect of fire has been to convert dwarf shrublands to grassland with the extirpation of several nonsprouters species. A collection of photographs describes this effect. It is anticipated that these nonsprouters will recolonise by seed over time, but could be eliminated if fire frequency is high enough to eliminate their seedbank. It is predicted that if grassy conditions persist in the Nama-Karoo, then fire will be an important factor that shapes the Nama-Karoo/grassland boundary. [ABSTRACT FROM AUTHOR]

Nama-Karoo vegetation is fire naïve and therefore vulnerable to transformation by fire. This study investigated the effect of fire, a novel disturbance, on the composition and structure of shrub communities in semi-arid Eastern Upper Karoo rangelands. Nine sites across a rainfall gradient had been burnt between eight years and six months before time of sampling, whose grazing history ranged from heavy or lenient to no grazing. Fire markedly changed the composition and structure of Karoo shrublands, the nature and extent of which depended on climate regime. Non-sprouting species, including some dominant species, were extirpated by fire and replaced by previously non-dominant sprouter species. Replacement of non-sprouter by sprouter species was conspicuous for palatable and unpalatable dwarf shrubs. Under conditions that closely resemble climate change forecasts for the region, fire transformed Nama-karoo shrublands. The possibility of larger more frequent fires in the Nama-Karoo threatens to transform the vegetation, ecosystem functioning, and economy of the region. Fire has emerged as a novel agent of vegetation change in the eastern Nama-Karoo owing to a directional increase in annual rainfall over the past three decades, that may cement a state change from shrubland to grassland in an ampliative, positive feedback manner. • Fire changes the composition of Nama-Karoo shrub communities. • The effect of Fire on Karoo shrub communities depends on mean annual rainfall which increases from East to West. • Abundant, non-sprouting species are eliminated by fire leading to drastic changes in shrub community composition. • The potential of fire to change Nama-Karoo vegetation has management implications for livestock production. • A positive feedback between rainfall and fire may lead to biome-shift from Nama-Karoo shrubland to grassland. [ABSTRACT FROM AUTHOR]

We used a near-complete phylogeny for the angiosperm clade Viburnum to assess lineage diversification rates, and to examine possible morphological and ecological factors driving radiations., Maximum-likelihood and Bayesian approaches identified shifts in diversification rate and possible links to character evolution. We inferred the ancestral environment for Viburnum and changes in diversification dynamics associated with subsequent biome shifts., Viburnum probably diversified in tropical forests of Southeast Asia in the Eocene, with three subsequent radiations in temperate clades during the Miocene. Four traits (purple fruits, extrafloral nectaries, bud scales and toothed leaves) were statistically associated with higher rates of diversification. However, we argue that these traits are unlikely to be driving diversification directly. Instead, two radiations were associated with the occupation of mountainous regions and a third with repeated shifts between colder and warmer temperate forests., Early-branching depauperate lineages imply that the rare lowland tropical species are 'dying embers' of once more diverse lineages; net diversification rates in Viburnum likely decreased in these tropical environments after the Oligocene. We suggest that 'taxon pulse' dynamics might characterize other temperate plant lineages. [ABSTRACT FROM AUTHOR]

Succession from fire-induced grassland to secondary shrubland vegetation is occurring in parts of deforested dry eastern South Island, New Zealand, but little is known about how the change from herbaceous to woody vegetation alters the indigenous biota. We predicted that development of secondary shrublands would exclude few grassland-specialist plant species and increase indigenous plant 'species occupancy' (the extent to which indigenous species capable of living in dryland landscapes are present) at a landscape scale. We also predicted that taller and denser indigenous plant canopies would facilitate indigenous but not exotic plant species at multiple scales, for example by reducing exotic grass competition or through positive plant-plant interactions. We tested our predictions by sampling vegetation in 100-ha blocks representing a gradient from grassland to mixed 'intermediate' grassland and shrubland to shrubland vegetation at three sites in Central Otago. We found indigenous plant species in shrubland were complementary to those in grassland (additional to the existing set) within and across our study sites, which led to higher indigenous species occupancy in this dryland landscape. Grassland vegetation did not support significant numbers of indigenous plant species complementary to those in shrubland, and we found no evidence that secondary succession displaced indigenous plant species. Shrubland had higher diversity of indigenous plant species than grassland at multiple scales (across sites, within 100-ha blocks and within 144-m2 plots), and had higher indigenous dominance of composition across sites, but not at smaller (within-block and within-plot) scales. Indigenous dominance of composition within blocks and plots was related to dominance of the physical structure of plant communities by indigenous woody plants or tussock grasses, rather than to development of secondary shrubland alone. Reduced densities of indigenous plant species were related to higher frequencies of exotic grass only where indigenous structural dominance was low, indicating that competitive exclusion of indigenous plants by exotic grasses may depend on degradation of indigenous structural dominance. We conclude that secondary succession from structurallydepleted grassland to mixed indigenous-exotic shrubland is likely to assist the conservation of indigenous plant species in this dryland landscape. [ABSTRACT FROM AUTHOR]

Highlights: [•] Tropical grassy biomes are extensive and critical to human livelihoods. [•] The definition of these grassy systems is inconsistent and misleading. [•] We discuss novel threats linked to problems with biome definition. [•] The assumption that ‘more trees are better’ does not hold for tropical grassy biomes. [Copyright &y& Elsevier]

The structure of tropical savanna ecosystems is influenced by fire frequency and intensity. There is particular interest in the extent to which long-term fire exclusion can result in a shift from savanna to forest vegetation that is not easily reversed by the reintroduction of fire. This study examined changes in the structure and composition of a long-unburnt site within the northern Australian savannas following an extended period of active fire exclusion (>20 years), and the effect of the reintroducing fire through experimental fire regimes, including fires in the early and late dry season at a range of frequencies. After the long period of fire exclusion, the vegetation community was characterized by a well-developed midstorey and canopy layer, low grass cover, substantially higher densities of woody sprouts and saplings than frequently burnt savanna. The community composition included a high proportion of rainforest-affiliated species. Three years of experimental fires had no detectable effect on the overall composition of grass layer and woody plants but had an effect on woody vegetation structure. Continued fire exclusion further increased the density of woody stems, particularly in the midstorey (2.0-4.99 m), whereas moderate-intensity fires (>800 kW m−1) significantly reduced the density of midstorey stems. The reintroduction of higher moderate intensity fire events resulted in the vegetation in some compartments reverting to the open savanna structure typical of frequently burnt sites. Such rapid reversibility suggests that in general, the woody thickening resulting from long-term fire exclusion did not represent a biome shift to a non-savanna state. However, there was a small proportion of the site that could not sustain the fires applied to them because grass cover was very low and patchy and therefore appeared to have crossed an ecological threshold towards closed forest. [ABSTRACT FROM AUTHOR]

Drought-induced tree mortality, which rapidly alters forest ecosystem composition, structure, and function, as well as the feedbacks between the biosphere and climate, has occurred worldwide over the past few decades, and is expected to increase pervasively as climate change progresses. The objectives of this review are to (1) highlight the likely ecological consequences of drought-induced tree mortality, (2) synthesize the hypotheses related to drought-induced tree mortality, (3) discuss the implications of current knowledge for modeling tree mortality processes under climate change, and (4) highlight future research needs. First, we emphasize the likely ecological consequences of tree mortality from ecosystem to biome to continental scales. We then document and criticize multiple non-exclusive tree mortality hypotheses (e.g., carbon starvation - carbon supply is less than carbon demand; and hydraulic failure - desiccation from failed water transport) from a more comprehensive ecological perspective. Next, we extend a forest decline concept model, Manion's framework, by considering new emerging environmental conditions, for a more thorough understanding of the effects of climate change on forest decline. We find that an increase in drought frequency and (or) climate-change-type droughts may trigger increased background tree mortality rates and severe forest dieback events, accelerating species turnover and ecological regime shifts. The contribution of CO2 fertilization, rising temperature within the optimal growth range, and increased nitrogen deposition may defer or reduce this trend in tree mortality, but such contributions will vary between locations, species, and tree sizes. Multiple hypotheses proposed for drought-induced tree mortality are discussed, but coupling carbon and water cycles could help resolve the debate. The absence of a physiological understanding of tree mortality mechanisms limits the predictive ability of current models from stand-level process-based models to dynamic global vegetation models. We thus suggest that long-term observations, experiments, and models should be tightly interwoven during the research process to better forecast future climate changes and evaluate their impacts on forests. [ABSTRACT FROM AUTHOR]

Aim Evidence is accumulating of a general increase in woody cover of many savanna regions of the world. Little is known about the consequences of this widespread and fundamental ecosystem structural shift on biodiversity. Location South Africa. Methods We assessed the potential response of bird species to shrub encroachment in a South African savanna by censusing bird species in five habitats along a gradient of increasing shrub cover, from grassland/open woodland to shrubland dominated by various shrub species. We also explored historical bird species population trends across southern Africa during the second half of the 20th century to determine if any quantifiable shifts had occurred that support an ongoing impact of shrub encroachment at the regional scale. Results At the local scale, species richness peaked at intermediate levels of shrub cover. Bird species composition showed high turnover along the gradient, suggesting that widespread shrub encroachment is likely to lead to the loss of certain species with a concomitant decline in bird species richness at the landscape scale. Finally, savanna bird species responded to changes in vegetation structure rather than vegetation species composition: bird assemblages were very similar in shrublands dominated by Acacia mellifera and those dominated by Tarchonanthus camphoratus. Main conclusions Shrub encroachment might have a bigger impact on bird diversity in grassland than in open woodland, regardless of the shrub species. Species recorded in our study area were associated with historical population changes at the scale of southern Africa suggesting that shrub encroachment could be one of the main drivers of bird population dynamics in southern African savannas. If current trends continue, the persistence of several southern African bird species associated with open savanna might be jeopardized regionally. [ABSTRACT FROM AUTHOR]

• A new phylogenetic hypothesis with improved sampling is presented for Calophyllaceae. • Our results show strong support for the HaCaKi clade (Haploclathra Caraipa + Kielmeyera • The monophyly of some clades is confirmed: Calophyllum, Kayea, Mammea and Neotropical clades. • Reproductive characters are related to evolutionary dynamic changes in Calophyllaceae. • The Andean uplift and temperature rise influenced diversification within Calophylleae. The clusioid clade comprises five monophyletic families: Bonnetiaceae, Calophyllaceae, Clusiaceae s.s., Hypericaceae, and Podostemaceae. Even though the circumscription of these families is well established, phylogenetic relationships within some families remain unresolved. This study aims to infer phylogenetic relationships within the Neotropical Calophylleae based on a broad sampling of taxa and a multilocus approach. We then use our phylogenetic framework as basis to investigate the evolution and biogeography of Calophylleae and diversification shifts in Calophyllaceae. To reconstruct the phylogeny of the Neotropical Calophylleae, we used five plastid (matK , ndhF , rbcL , psbA - trnH , and trnK), two mitochondrial (matR and rps3), and two nuclear (EMB2765 and ITS) markers, including previously published and newly generated sequences. We sampled 74 species, increasing sampling of Neotropical taxa by 500%. Our phylogenetic hypothesis for Calophyllaceae provides additional support for the monophyly of all genera and allowed us to identify four main clades: Calophyllum, Kayea, Mammea, and the Neotropical clade. The Neotropical clade includes three main lineages, a small clade composed of Clusiella and Marila , and a large HaCaKi clade (i.e., Haplocarpa , Caraipa , and Kilmeyera) that is sister to Mahurea exstipulata. The evolution of three morphological traits (i.e., fleshy fruits, anther glands, and winged seeds) were shown to be associated with changes in evolutionary dynamics in Calophyllaceae, while a biome shift was detected in Kielmeyera , affecting net diversification within this genus. Major geological and climatic events such as the Andean uplift and a gradual decrease in temperatures seem to have influenced diversification rates within the Neotropical Calophylleae. [ABSTRACT FROM AUTHOR]